The Yaquina Estuary has strong seasonal variation in the magnitude of nutrient loading 
and in the dominant nutrient sources. Response variables (particularly, chlorophyll a and 
dissolved oxygen) exhibited similar patterns of seasonal variation. During the wet season 
(November-April), riverine nitrogen inputs dominate, whereas during the dry season (May - 
October) oceanic nitrogen sources dominate. Riverine inputs are primarily related to the 
presence of nitrogen-fixing red alder (Alnus rubra) trees in the watershed. There are also strong 
zonal differences in nutrient levels, response variables, and dominant nutrient sources within the 
Yaquina Estuary. In the lower estuary (Zone 1), water quality conditions are strongly influenced 
by ocean conditions, while in the upper portions of the estuary (Zone 2), watershed and point 
source inputs increase in importance. 
We suggest that criteria be developed for wet and dry seasons to address the strong 
seasonal variation in nutrient loads and sources. Dry season criteria (May-October) are most 
important, since during the wet season, there appears to be little utilization of nutrients within the 
estuary, and chlorophyll a levels are low and the dissolved oxygen concentrations are high. 
Thus, it is not clear that wet season criteria are needed within the Yaquina Estuary. We suggest 
that separate criteria be developed for Zones 1 and 2, with dry season criteria for Zone 2 a first 
priority. The high degree of ocean-estuary coupling found for Zone 1 within the Yaquina 
Estuary with associated short-term variability in water quality parameters suggests that 
monitoring for compliance with nutrient criteria in this region may be problematic. During the 
dry season, phosphate, nitrate, chlorophyll a , and dissolved oxygen levels in Zone 1 are primarily 
determined by ocean conditions and separation of oceanic from anthropogenic inputs would 
require, at the least, continuous monitoring capability, and may require additional techniques. 
Use of Total Suspended Solids (TSS) as a water quality criterion may not be practical due 
to inconsistent spatial and temporal patterns relative to that of adjacent Oregon estuaries. 
Macroalgal biomass response within Yaquina Estuary appears to be primarily driven by oceanic 
nitrogen input, and thus does not appear to be useful as an indicator of cultural eutrophication. 
Based on weight of scientific evidence, we conclude that Yaquina Estuary is not 
exhibiting symptoms of cultural eutrophication. Thus, following the recommendations in U.S. 
EPA (2001), median values could be used as criteria for most water quality parameters. The 
Seagrass Stress-Response Model confirmed that the median percentile for water clarity (kj) 
would be protective of the existing eelgrass (.Zoster a marina) habitat in the Yaquina Estuary. 
IV 
